From: Olivier Fisette Date: Thu, 23 Dec 2004 21:19:57 +0000 (+0000) Subject: Moved from app-sci/cutg to sci-biology/cutg. X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=e36ad954d9e5cf7ada4642bf53a0f07fbad5c5ce;p=gentoo.git Moved from app-sci/cutg to sci-biology/cutg. --- diff --git a/sci-biology/cutg/ChangeLog b/sci-biology/cutg/ChangeLog new file mode 100644 index 000000000000..99f12437ffbd --- /dev/null +++ b/sci-biology/cutg/ChangeLog @@ -0,0 +1,43 @@ +# ChangeLog for app-sci/cutg +# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/cutg/ChangeLog,v 1.1 2004/12/23 21:19:57 ribosome Exp $ + +*cutg-143 (23 Dec 2004) + + 23 Dec 2004; Olivier Fisette +metadata.xml, + +cutg-143.ebuild, +cutg-144.ebuild: + Moved from app-sci/cutg to sci-biology/cutg. + +*cutg-144 (23 Nov 2004) + + 23 Nov 2004; Olivier Fisette +cutg-144.ebuild: + New version. + + 31 Oct 2004; Olivier Fisette -cutg-142.ebuild, + cutg-143.ebuild: + Removed old version. Added 143 to x86. + +*cutg-143 (29 Sep 2004) + + 29 Sep 2004; Olivier Fisette -cutg-141.0.ebuild, + cutg-142.ebuild, +cutg-143.ebuild: + Added 142 to x86. Added new version 142. Removed old version. + +*cutg-142 (10 Aug 2004) + + 10 Aug 2004; Olivier Fisette + cutg-141.0.ebuild: + Added to x86. + cutg-142.ebuild: + Updated package. + + 26 Jun 2004; David Holm cutg-141.0.ebuild: + Added to ~ppc. + +*cutg-141.0 (24 Jun 2004) + + 24 Jun 2004; Olivier Fisette + cutg-141.0.ebuild, metadata.xml : + Initial import. Ebuild submitted by Olivier Fisette . + Reference: Gentoo Bugzilla, bug #54322 + diff --git a/sci-biology/cutg/Manifest b/sci-biology/cutg/Manifest new file mode 100644 index 000000000000..d81a49b14c73 --- /dev/null +++ b/sci-biology/cutg/Manifest @@ -0,0 +1,6 @@ +MD5 e4a9cb7a750c45b5f064e0791a6db623 cutg-143.ebuild 1178 +MD5 2bb31e68b962982d6890f9636a4bac63 ChangeLog 1115 +MD5 d14f29edef39d8d89b39a5787c3d141c metadata.xml 594 +MD5 3e219869a7440d22d1a3e3b6605429f4 cutg-144.ebuild 1179 +MD5 94ad06877dbe9065273a7ee15904c7ec files/digest-cutg-143 63 +MD5 e35ab30eae79e0600feabc028e0db162 files/digest-cutg-144 63 diff --git a/sci-biology/cutg/cutg-143.ebuild b/sci-biology/cutg/cutg-143.ebuild new file mode 100644 index 000000000000..8dbbe5af181a --- /dev/null +++ b/sci-biology/cutg/cutg-143.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2004 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/cutg/cutg-143.ebuild,v 1.1 2004/12/23 21:19:57 ribosome Exp $ + +DESCRIPTION="Codon usage tables calculated from GenBank" +HOMEPAGE="http://www.kazusa.or.jp/codon/" +SRC_URI="ftp://ftp.kazusa.or.jp/pub/codon/current/compressed/CUTG.${PV}.tar.gz" +LICENSE="public-domain" + +SLOT="0" +KEYWORDS="x86 ~ppc" +IUSE="no-emboss no-rawdb" + +S=${WORKDIR} + +src_compile() { + # Index the database for use with emboss if emboss is installed and + # the user did not explicitly request not to index the database. + if [ -e /usr/bin/cutgextract ] && ! use no-emboss; then + mkdir CODONS + einfo "Indexing CUTG for usage with EMBOSS." + EMBOSS_DATA=. cutgextract -auto -directory ${S} || die \ + "Indexing CUTG failed." + fi +} + +src_install() { + if ! use no-rawdb; then + mkdir -p ${D}/usr/share/${PN} + mv *.codon *.spsum ${D}/usr/share/${PN} + fi + dodoc README + if [ -e /usr/bin/cutgextract ] && ! use no-emboss; then + mkdir -p ${D}/usr/share/EMBOSS/data/CODONS + cd CODONS + for file in *; do + mv ${file} ${D}/usr/share/EMBOSS/data/CODONS + done + fi +} diff --git a/sci-biology/cutg/cutg-144.ebuild b/sci-biology/cutg/cutg-144.ebuild new file mode 100644 index 000000000000..46b0aaceef27 --- /dev/null +++ b/sci-biology/cutg/cutg-144.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2004 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/cutg/cutg-144.ebuild,v 1.1 2004/12/23 21:19:57 ribosome Exp $ + +DESCRIPTION="Codon usage tables calculated from GenBank" +HOMEPAGE="http://www.kazusa.or.jp/codon/" +SRC_URI="ftp://ftp.kazusa.or.jp/pub/codon/current/compressed/CUTG.${PV}.tar.gz" +LICENSE="public-domain" + +SLOT="0" +KEYWORDS="~x86 ~ppc" +IUSE="no-emboss no-rawdb" + +S=${WORKDIR} + +src_compile() { + # Index the database for use with emboss if emboss is installed and + # the user did not explicitly request not to index the database. + if [ -e /usr/bin/cutgextract ] && ! use no-emboss; then + mkdir CODONS + einfo "Indexing CUTG for usage with EMBOSS." + EMBOSS_DATA=. cutgextract -auto -directory ${S} || die \ + "Indexing CUTG failed." + fi +} + +src_install() { + if ! use no-rawdb; then + mkdir -p ${D}/usr/share/${PN} + mv *.codon *.spsum ${D}/usr/share/${PN} + fi + dodoc README + if [ -e /usr/bin/cutgextract ] && ! use no-emboss; then + mkdir -p ${D}/usr/share/EMBOSS/data/CODONS + cd CODONS + for file in *; do + mv ${file} ${D}/usr/share/EMBOSS/data/CODONS + done + fi +} diff --git a/sci-biology/cutg/files/digest-cutg-143 b/sci-biology/cutg/files/digest-cutg-143 new file mode 100644 index 000000000000..55572f7df18e --- /dev/null +++ b/sci-biology/cutg/files/digest-cutg-143 @@ -0,0 +1 @@ +MD5 8f3ccb3c31e1383ac987d8e46c9f5610 CUTG.143.tar.gz 117357602 diff --git a/sci-biology/cutg/files/digest-cutg-144 b/sci-biology/cutg/files/digest-cutg-144 new file mode 100644 index 000000000000..f79c6a6dc995 --- /dev/null +++ b/sci-biology/cutg/files/digest-cutg-144 @@ -0,0 +1 @@ +MD5 2bea63f0124ef7cb360bddeb0465e548 CUTG.144.tar.gz 124856915 diff --git a/sci-biology/cutg/metadata.xml b/sci-biology/cutg/metadata.xml new file mode 100644 index 000000000000..b89e0f65dac4 --- /dev/null +++ b/sci-biology/cutg/metadata.xml @@ -0,0 +1,16 @@ + + + + + ribosome@gentoo.org + Olivier Fisette + + sci + + Codon usage tables maintained at the Kazusa DNA Research Institute. + Codon usage in individual genes has been calculated using the + nucleotide sequence data obtained from the GenBank Genetic Sequence + Database. The compilation of codon usage is synchronized with each + major release of GenBank. + +